chr20-5198933-A-G

Variant names:

• chr20-5198933-A-G
• rs6053189

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.309 in 152,122 control chromosomes in the GnomAD database, including 7,760 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.31 (7760 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.284
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46913 AN: 152004 Hom.: 7754 Cov.: 33

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.307

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.309 AC: 46935 AN: 152122 Hom.: 7760 Cov.: 33 AF XY: 0.305 AC XY: 22675 AN XY: 74350

African (AFR) AF: 0.221 AC: 9159 AN: 41504

American (AMR) AF: 0.260 AC: 3982 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1207 AN: 3470

East Asian (EAS) AF: 0.135 AC: 698 AN: 5172

South Asian (SAS) AF: 0.372 AC: 1795 AN: 4820

European-Finnish (FIN) AF: 0.331 AC: 3496 AN: 10574

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.376 AC: 25585 AN: 67966

Other (OTH) AF: 0.305 AC: 645 AN: 2112

Alfa AF: 0.330 Hom.: 1098

Bravo AF: 0.296

Asia WGS AF: 0.231 AC: 803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.85
DANN	Benign	0.78
PhyloP100		-0.28

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6053189; hg19: chr20-5179579;